Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability. - John H. Reif; Thomas H. LaBean; Michael Pirrung; Vipul S. Rana; Bo Guo; Carl Kingsford; Gene S. Wickham (DNA, 2001)

The Side-Chain Positioning Problem: A Semidefinite Programming Formulation With New Rounding Schemes. - Bernard Chazelle; Carl Kingsford; Mona Singh 001 (PCK50, 2003)

A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies. - Bernard Chazelle; Carl Kingsford; Mona Singh 001 (INFORMS J. Comput., 2004)

Solving and analyzing side-chain positioning problems using linear and integer programming. - Carleton Kingsford; Bernard Chazelle; Mona Singh 001 (Bioinform., 2005)

A Compact Mathematical Programming Formulation for DNA Motif Finding. - Carl Kingsford; Elena Zaslavsky; Mona Singh 001 (CPM, 2006)

Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques. - Niranjan Nagarajan; Carl Kingsford (BIBM, 2008)

A cooperative combinatorial Particle Swarm Optimization algorithm for side-chain packing. - Grecia Lapizco-Encinas; Carl Kingsford; James A. Reggia (SIS, 2009)

Revealing Biological Modules via Graph Summarization. - Saket Navlakha; Michael C. Schatz; Carl Kingsford (J. Comput. Biol., 2009)

Particle Swarm Optimization for multimodal combinatorial problems and its application to protein design. - Grecia Lapizco-Encinas; Carl Kingsford; James A. Reggia (IEEE Congress on Evolutionary Computation, 2010)

Exploring Biological Network Dynamics with Ensembles of Graph Partitions. - Saket Navlakha; Carl Kingsford (Pacific Symposium on Biocomputing, 2010)

The power of protein interaction networks for associating genes with diseases. - Saket Navlakha; Carl Kingsford (Bioinform., 2010)

Assembly complexity of prokaryotic genomes using short reads. - Carl Kingsford; Michael C. Schatz; Mihai Pop (BMC Bioinform., 2010)

Alignment and clustering of phylogenetic markers - implications for microbial diversity studies. - James Robert White; Saket Navlakha; Niranjan Nagarajan; Mohammadreza Ghodsi; Carl Kingsford; Mihai Pop (BMC Bioinform., 2010)

Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information. - Saket Navlakha; James Robert White; Niranjan Nagarajan; Mihai Pop; Carl Kingsford (J. Comput. Biol., 2010)

Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction. - Emre Sefer; Carl Kingsford (RECOMB, 2011)

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. - Guillaume Marçais; Carl Kingsford (Bioinform., 2011)

Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. - Joshua L. Wetzel; Carl Kingsford; Mihai Pop (BMC Bioinform., 2011)

Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression. - David R. Kelley; Carl Kingsford (J. Comput. Biol., 2011)

A cost-aggregating integer linear program for motif finding. - Carl Kingsford; Elena Zaslavsky; Mona Singh 001 (J. Discrete Algorithms, 2011)

Network Archaeology: Uncovering Ancient Networks from Present-Day Interactions. - Saket Navlakha; Carl Kingsford (PLoS Comput. Biol., 2011)

Review of Complex social networks by Fernando Vega-Redondo. - Carl Kingsford (SIGACT News, 2011)

The missing models: a data-driven approach for learning how networks grow. - Rob Patro; Geet Duggal; Emre Sefer; Hao Wang 024; Darya Filippova; Carl Kingsford (KDD, 2012)

Dynamic Exploration of Recording Sessions between Jazz Musicians over Time. - Darya Filippova; Michael Fitzgerald; Carl Kingsford; Fernando Benadon (SocialCom/PASSAT, 2012)

Resolving Spatial Inconsistencies in Chromosome Conformation Data. - Geet Duggal; Rob Patro; Emre Sefer; Hao Wang 024; Darya Filippova; Samir Khuller; Carl Kingsford (WABI, 2012)

Parsimonious reconstruction of network evolution. - Rob Patro; Emre Sefer; Justin Malin; Guillaume Marçais; Saket Navlakha; Carl Kingsford (Algorithms Mol. Biol., 2012)

Global network alignment using multiscale spectral signatures. - Rob Patro; Carl Kingsford (Bioinform., 2012)

Graph rigidity reveals well-constrained regions of chromosome conformation embeddings. - Geet Duggal; Carl Kingsford (BMC Bioinform., 2012)

Coral: an integrated suite of visualizations for comparing clusterings. - Darya Filippova; Aashish Gadani; Carl Kingsford (BMC Bioinform., 2012)

Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin. - Hao Wang 024; Geet Duggal; Rob Patro; Michelle Girvan; Sridhar Hannenhalli; Carl Kingsford (BCB, 2013)

Multiscale Identification of Topological Domains in Chromatin. - Darya Filippova; Rob Patro; Geet Duggal; Carl Kingsford (WABI, 2013)

Resolving spatial inconsistencies in chromosome conformation measurements. - Geet Duggal; Rob Patro; Emre Sefer; Hao Wang 024; Darya Filippova; Samir Khuller; Carl Kingsford (Algorithms Mol. Biol., 2013)

Predicting protein interactions via parsimonious network history inference. - Rob Patro; Carl Kingsford (Bioinform., 2013)

Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms. - Rob Patro; Stephen M. Mount; Carl Kingsford (CoRR, 2013)

Diffusion Archaeology for Diffusion Progression History Reconstruction. - Emre Sefer; Carl Kingsford (ICDM, 2014)

Identification of alternative topological domains in chromatin. - Darya Filippova; Rob Patro; Geet Duggal; Carl Kingsford (Algorithms Mol. Biol., 2014)

Rapid, separable compression enables fast analyses of sequence alignments. - Darya Filippova; Carl Kingsford (BCB, 2015)

Convex Risk Minimization to Infer Networks from probabilistic diffusion data at multiple scales. - Emre Sefer; Carl Kingsford (ICDE, 2015)

Reference-based compression of short-read sequences using path encoding. - Carl Kingsford; Rob Patro (Bioinform., 2015)

Data-dependent bucketing improves reference-free compression of sequencing reads. - Rob Patro; Carl Kingsford (Bioinform., 2015)

Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping. - Hongyi Xin; John Greth; John Emmons; Gennady Pekhimenko; Carl Kingsford; Can Alkan; Onur Mutlu (Bioinform., 2015)

The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB). - Farhad Hormozdiari; Fereydoun Hormozdiari; Carl Kingsford; Paul Medvedev; Fabio Vandin (RECOMB, 2016)

Improving Bloom Filter Performance on Sequence Data Using k -mer Bloom Filters. - David Pellow; Darya Filippova; Carl Kingsford (RECOMB, 2016)

Compact Universal k-mer Hitting Sets. - Yaron Orenstein; David Pellow; Guillaume Marçais; Ron Shamir; Carl Kingsford (WABI, 2016)

Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap. - Hao Wang 024; Joel McManus; Carl Kingsford (Bioinform., 2016)

Optimal seed solver: optimizing seed selection in read mapping. - Hongyi Xin; Sunny Nahar; Richard L. Zhu; John Emmons; Gennady Pekhimenko; Carl Kingsford; Can Alkan; Onur Mutlu (Bioinform., 2016)

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin. - Rob Patro; Raquel Norel; Robert J. Prill; Julio Saez-Rodriguez; Peter Lorenz; Felix Steinbeck; Bjoern Ziems; Mitja Lustrek; Nicola Barbarini; Alessandra Tiengo; Riccardo Bellazzi; Hans-Jürgen Thiesen; et al. (BMC Bioinform., 2016)

Efficient Index Maintenance Under Dynamic Genome Modification. - Nitish Gupta; Komal Sanjeev; Tim Wall; Carl Kingsford; Rob Patro (CoRR, 2016)

Teaching Computation to Biologists. - Carl Kingsford (Comput. Sci. Eng., 2016)

Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations. - Emre Sefer; Geet Duggal; Carl Kingsford (J. Comput. Biol., 2016)

Diffusion archeology for diffusion progression history reconstruction. - Emre Sefer; Carl Kingsford (Knowl. Inf. Syst., 2016)

Improving the performance of minimizers and winnowing schemes. - Guillaume Marçais; David Pellow; Daniel Bork; Yaron Orenstein; Ron Shamir; Carl Kingsford (Bioinform., 2017)

Improving Bloom Filter Performance on Sequence Data Using k-mer Bloom Filters. - David Pellow; Darya Filippova; Carl Kingsford (J. Comput. Biol., 2017)

Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast. - Hao Wang 024; Joel McManus; Carl Kingsford (J. Comput. Biol., 2017)

Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing. - Yaron Orenstein; David Pellow; Guillaume Marçais; Ron Shamir; Carl Kingsford (PLoS Comput. Biol., 2017)

Asymptotically optimal minimizers schemes. - Guillaume Marçais; Dan F. DeBlasio; Carl Kingsford (Bioinform., 2018)

Quantifying the similarity of topological domains across normal and cancer human cell types. - Natalie Sauerwald; Carl Kingsford (Bioinform., 2018)

Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees. - Brad Solomon; Carl Kingsford (J. Comput. Biol., 2018)

Practical Universal k-mer Sets for Minimizer Schemes. - Dan F. DeBlasio; Fiyinfoluwa Gbosibo; Carl Kingsford; Guillaume Marçais (BCB, 2019)

Collective Model Fusion for Multiple Black-Box Experts. - Quang Minh Hoang; Trong Nghia Hoang; Bryan Kian Hsiang Low; Carl Kingsford (ICML, 2019)

Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation. - Natalie Sauerwald; Yihang Shen; Carl Kingsford (WABI, 2019)

Semi-nonparametric modeling of topological domain formation from epigenetic data. - Emre Sefer; Carl Kingsford (Algorithms Mol. Biol., 2019)

Locality-sensitive hashing for the edit distance. - Guillaume Marçais; Dan F. DeBlasio; Prashant Pandey 001; Carl Kingsford (Bioinform., 2019)

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. - Michael P. Snyder; Shin Lin; Amanda Posgai; Mark Atkinson; Aviv Regev; Jennifer Rood; Orit Rozenblatt-Rosen; Leslie Gaffney; Anna Hupalowska; Rahul Satija; Nils Gehlenborg; Jay Shendure; et al. (Nat., 2019)

Theory and A Heuristic for the Minimum Path Flow Decomposition Problem. - Mingfu Shao; Carl Kingsford (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Optimizing Dynamic Structures with Bayesian Generative Search. - Minh Hoang; Carleton Kingsford (ICML, 2020)

Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem. - Yutong Qiu; Cong Ma 008; Han Xie; Carl Kingsford (Algorithms Mol. Biol., 2020)

Context-aware seeds for read mapping. - Hongyi Xin; Mingfu Shao; Carl Kingsford (Algorithms Mol. Biol., 2020)

Improved design and analysis of practical minimizers. - Hongyu Zheng 001; Carl Kingsford; Guillaume Marçais (Bioinform., 2020)

More Accurate Transcript Assembly via Parameter Advising. - Dan F. DeBlasio; Kwanho Kim; Carl Kingsford (J. Comput. Biol., 2020)

How much data is sufficient to learn high-performing algorithms? generalization guarantees for data-driven algorithm design. - Maria-Florina Balcan; Dan F. DeBlasio; Travis Dick; Carl Kingsford; Tuomas Sandholm; Ellen Vitercik (STOC, 2021)

Exact transcript quantification over splice graphs. - Cong Ma 008; Hongyu Zheng 001; Carl Kingsford (Algorithms Mol. Biol., 2021)

Constructing small genome graphs via string compression. - Yutong Qiu; Carl Kingsford (Bioinform., 2021)

Maximum likelihood reconstruction of ancestral networks by integer linear programming. - Vaibhav Rajan; Ziqi Zhang; Carl Kingsford; Xiuwei Zhang 002 (Bioinform., 2021)

Practical selection of representative sets of RNA-seq samples using a hierarchical approach. - Laura H. Tung; Carl Kingsford (Bioinform., 2021)

Sequence-specific minimizers via polar sets. - Hongyu Zheng 001; Carl Kingsford; Guillaume Marçais (Bioinform., 2021)

Harvestman: a framework for hierarchical feature learning and selection from whole genome sequencing data. - Trevor S. Frisby; Shawn J. Baker; Guillaume Marçais; Quang Minh Hoang; Carl Kingsford; Christopher J. Langmead (BMC Bioinform., 2021)

Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length. - Hongyu Zheng 001; Carl Kingsford; Guillaume Marçais (J. Comput. Biol., 2021)

DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes. - Minh Hoang; Hongyu Zheng 001; Carl Kingsford (RECOMB, 2022)

The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance. - Yutong Qiu; Carl Kingsford (Bioinform., 2022)

Differentiable Learning of Sequence-Specific Minimizer Schemes with DeepMinimizer. - Minh Hoang; Hongyu Zheng 001; Carl Kingsford (J. Comput. Biol., 2022)

Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability. - Hongyu Zheng 001; Cong Ma 008; Carl Kingsford (J. Comput. Biol., 2022)

Computationally Efficient High-Dimensional Bayesian Optimization via Variable Selection. - Yihang Shen; Carl Kingsford (AutoML, 2023)

Reinforcement Learning for Robotic Liquid Handler Planning. - Mohsen Ferdosi; Yuejun Ge; Carl Kingsford (WABI, 2023)

Creating and Using Minimizer Sketches in Computational Genomics. - Hongyu Zheng 001; Guillaume Marçais; Carl Kingsford (J. Comput. Biol., 2023)

Efficient Heterogeneous Meta-Learning via Channel Shuffling Modulation. - Minh Hoang; Carl Kingsford (ICLR, 2024)

A Scalable Optimization Algorithm for Solving the Beltway and Turnpike Problems with Uncertain Measurements. - C. S. Elder; Minh Hoang; Mohsen Ferdosi; Carl Kingsford (RECOMB, 2024)

Graph-Based Genome Inference from Hi-C Data. - Yihang Shen; Lingge Yu; Yutong Qiu; Tianyu Zhang; Carl Kingsford (RECOMB, 2024)

Approximate and Exact Optimization Algorithms for the Beltway and Turnpike Problems with Duplicated, Missing, Partially Labeled, and Uncertain Measurements. - C. S. Elder; Minh Hoang; Mohsen Ferdosi; Carl Kingsford (J. Comput. Biol., 2024)

Sketching Methods with Small Window Guarantee Using Minimum Decycling Sets. - Guillaume Marçais; Dan F. DeBlasio; Carl Kingsford (J. Comput. Biol., 2024)

Density and Conservation Optimization of the Generalized Masked-Minimizer Sketching Scheme. - Minh Hoang; Guillaume Marçais; Carl Kingsford (J. Comput. Biol., 2024)

How Much Data Is Sufficient to Learn High-Performing Algorithms? - Maria-Florina Balcan; Dan F. DeBlasio; Travis Dick; Carl Kingsford; Tuomas Sandholm; Ellen Vitercik (J. ACM, 2024)

Revisiting the complexity of and algorithms for the graph traversal edit distance and its variants. - Yutong Qiu; Yihang Shen; Carl Kingsford (Algorithms Mol. Biol., 2024)

A synthesis for uniformly 3-edge-connected graphs. - Carl Kingsford; Guillaume Marçais (Discret. Appl. Math., 2025)